Afraid not. This isn't a "problem" with Mail per se, or any other email client for that matter. Your Gmail is web-based and maintained by Google, not by Mail or any other client on your computer. Mail cannot distinguish between old and new messages with Gmail so all it essentially does is synchronize with Google.

The only way to keep Mail from dowloading your replies sent earlier is to delete them off the server first. You don't have this "problem" with normal POP email because replies aren't saved on the server to begin with... they are saved on your computer.